Modeling superhelical DNA: recent analytical and dynamic approaches

Research output: Contribution to journalArticlepeer-review

Abstract

During the past year, a variety of diverse and complementary approaches have been presented for modeling superhelical DNA, offering new physical and biological insights into fundamental functional processes of DNA. Analytical approaches have probed deeper into the effects of entropy and thermal fluctuations on DNA structure and on various topological constraints induced by DNA-binding proteins. In tandem, new kinetic approaches - by molecular, Langevin and Brownian dynamics, as well as extensions of elastic-rod theory - have begun to offer dynamic information associated with supercoiling. Such dynamic approaches, along with other equilibrium studies, are refining the basic elastic-rod and polymer framework and incorporating more realistic treatments of salt and sequence-specific features. These collective advances in modeling large DNA molecules, in concert with technological innovations, are pointing to an exciting interplay between theory and experiment on the horizon.

Original languageEnglish (US)
Pages (from-to)245-262
Number of pages18
JournalCurrent Opinion in Structural Biology
Volume5
Issue number2
DOIs
StatePublished - Apr 1995

Keywords

  • MD molecular dynamics
  • bp base pair

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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